- Docker:
docker pull nipreps/mriqc:26.1.0(linux/amd64 and linux/arm64) - PyPI:
pip install mriqc==26.1.0(Python 3.13 or newer)
The first minor release of the 26.x series.
MRIQC now supports FLAIR images, and a fix to the head mask changes the background IQMs of every anatomical run.
With thanks to @cooper-sharp for their first contribution (FLAIR support), to @celprov for the summary of the DWI report, and to @asaraog, @DimitriPapadopoulos, @jdotc1 and @jhlegarreta, whose pull requests and proposals some of the changes below build on.
Highlights
- FLAIR images:
*_FLAIRruns go through the anatomical workflow, which normalizes them to the T2w template, and get participant and group reports (#1438). FLAIR IQMs are not uploaded to the MRIQC Web API. - A head mask that keeps the brain: since 23.1.0, every head mask included the two outermost sagittal planes, and where the field of view cut the brain, the brain fell into the background (#1479).
- BIDS inheritance: metadata set only in top-level sidecars (for example,
RepetitionTimeintask-rest_bold.json) now reaches the workflows (#1471). - DataLad in the container image: the image installs a working boto3 again, so runs on DataLad datasets no longer need
--no-datalad-get(#1478).
Backward-incompatible changes
- The background IQMs of every anatomical run change:
summary_bg_*,snrd_*,fberandqi_2. On five T1w runs of ds007486, the median changes were +7% forfber, +1% forsnrd_totaland −28% forqi_2. Where the field of view cuts the brain, as in reduced-FoV FLAIR, they change much more, and so doescnr. Do not mix anatomical IQMs from 26.0 and 26.1 within a study. - FLAIR runs are processed by default when a dataset has them. Pass
-m T1w T2w bold dwito keep the 26.0 selection. - Anatomical runs with more than one volume are dropped with a warning. The check never applied to T1w and T2w before (#1474).
- A BIDS database written by an earlier version keeps its old index, without the top-level sidecars: pass
--bids-database-wipewhen rerunning into an existing output folder (#1471). - The
abide2bidscommand is removed (it had failed on import since 24.0). The usage guide now has a table of where each ABIDE subject lives in DataLad's///abide(#1470).
Changes
- FIX: Head mask cutting through brain with narrow FoV anatomicals by @oesteban (#1479)
- FIX: Keep
Harmonizefrom emptying the image and apply the single-volume check to T1w/T2w by @oesteban (#1474) - FIX: Index top-level sidecars so BIDS metadata inheritance works by @oesteban (#1471)
- FIX: Cap
python-dateutilso the image resolves a working boto3 by @oesteban (#1478) - FIX: List every output BIDS does not define in
.bidsignoreby @oesteban, building on work by @asaraog (#1480, #1448) - ENH: Add FLAIR as a supported anatomical modality by @cooper-sharp (#1438)
- ENH: Add a textual summary to the DWI report by @celprov (#1291)
- MAINT: Replace the
abide2bidsscript with a table of ABIDE locations in DataLad by @oesteban, superseding a fix by @jdotc1 (#1470, #1451) - MAINT: Fail pytest on warnings by @oesteban, after a proposal by @jhlegarreta (#1472, #1370)
- MAINT: Run
build,twine,hatchand ruff with uv instead of pipx by @oesteban, after a proposal by @DimitriPapadopoulos (#1473, #1419)
Author list for papers based on MRIQC 26.1 series
As described in the Contributor Guidelines, anyone listed as a developer or contributor may write and submit manuscripts about MRIQC. To do so, please move the author(s) name(s) to the front of the following list:
Christopher J. Markiewicz 1; Zvi Baratz 2; Céline Provins 3; Eilidh MacNicol 4; Dimitri Papadopoulos Orfanos 5; Teresa Gomez 6; Dylan Nielson 7; Jan Varada 8; Ross W. Blair 1; McKenzie P. Hagen 9; William Triplett 10; Jon Haitz Legarreta Gorroño 11; Mathias Goncalves 1; Nikita Beliy 12; John A. Lee 13; Patrick Sadil 14; Ursula A. Tooley 15; Yaroslav O. Halchenko 16; Yibei Chen 17; James D. Kent 18; Bennet Fauber 19; Taylor Salo 20; Michael Krause 21; Pablo Velasco 22; Thomas Nichols 23; Victor Férat 24; Adam Huffman 25; Elodie Savary 3; Johannes Achtzehn 26; Joke Durnez 1; Satrajit S. Ghosh 27; Adam C. Raikes 28; Asier Erramuzpe 29; Benjamin Kay 30; Daniel Birman 1; Michael Dayan 31; Michael G. Clark 32; Rafael Garcia-Dias 33; Adam G. Thomas 34; Russell A. Poldrack 1; Ariel Rokem 6; Oscar Esteban 35.
Affiliations:
- Department of Psychology, Stanford University, CA, USA
- Quantivly Inc., Somerville, MA, USA
- Department of Radiology, Lausanne University Hospital and University of Lausanne, Switzerland
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NeuroSpin, CEA, Université Paris-Saclay, NeuroSpin, Gif-sur-Yvette, France
- The University of Washington eScience Institute, WA, USA
- Section on Clinical and Computational Psychiatry, National Institute of Mental Health, Bethesda, MD, USA
- Functional MRI Facility, National Institute of Mental Health, Bethesda, MD, USA
- Psychology Department, University of Washington, Seattle, WA, USA
- University of Florida: Gainesville, Florida, US
- Brigham and Women's Hospital, Mass General Brigham, Harvard Medical School, MA, USA
- CRC ULiege, Liege, Belgium
- Quansight, Dublin, Ireland
- Johns Hopkins Bloomberg School of Public Health, MD, USA
- Department of Neuroscience, University of Pennsylvania, PA, USA
- Psychological and Brain Sciences Department, Dartmouth College, NH, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, USA
- Department of Psychology, University of Texas at Austin, TX, USA
- University of Michigan, Ann Arbor, USA
- Department of Psychology, Florida International University, FL, USA
- Max Planck Institute for Human Development, Berlin, Germany
- Center for Brain Imaging, New York University, NY, USA
- Oxford Big Data Institute, University of Oxford, Oxford, GB
- Department of Basic Neurosciences, Université de Genève, Geneva, Switzerland
- Department of Physics, Imperial College London, London, UK
- Charité Berlin, Berlin, Germany
- McGovern Institute for Brain Research, MIT, MA, USA; and Department of Otolaryngology, Harvard Medical School, MA, USA
- Center for Innovation in Brain Science, University of Arizona, Tucson, AZ, USA
- Computational Neuroimaging Lab, BioCruces Health Research Institute
- Washington University School of Medicine, St.Louis, MO, USA
- International Committee of the Red Cross - ICRC, Geneva, Switzerland
- National Institutes of Health, USA
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- Data Science and Sharing Team, National Institute of Mental Health, Bethesda, MD, USA
- School of Engineering, HES-SO Valais/Wallis, Sion, Switzerland